• How to use R Markdown? Tutorial with example document.
• How to use Git and Github for version control?

• A few students were added from the waitlist.
• Waitlist is now closed and further is no longer active for Fall 2018 term.
• Unlikely to be added after this week.

Please go to this link NOW (if you have not already) and submit you Github username:

http://bit.ly/githubmds

Office hours of TAs now set as well.

Instructor: Thomas Brambor
thomas.brambor@columbia.edu
IAB 509E Mon 4.50 - 5.50pm

TA1: Crystal Ni
xn2115@tc.columbia.edu
IAB 270J Thur 10am - 12pm

TA2: Mikaela Zhang
xz2782@columbia.edu
IAB 270J Tue 10am - 12pm

• To allow advanced students or students with interest in specific topics to go a bit further than what is covered in the course, I am including a section called Advanced Topics (optional, on your own only) on the syllabus for each week.
  
• Feel free to completely ignore these sections!
  
• These sections are meant to be autodidactive. The TAs and myself are first and foremost concerned with the material covered in the course.

• For credit, graded: Required to hand in all exercises and complete the final project/exam.

• Pass-Fail: Same process as graded students. I submit a letter grade which the registrar converts to either P or F.

• R registered students (audit):
  • Complete 2 of the assignments from week 3 or later.
    
  • No need to complete final project.

Source: R Studio Webinar "Introducing Notebooks with R Markdown"

Source: R Studio Webinar "Introducing Notebooks with R Markdown"

Source: R Studio Webinar "Introducing Notebooks with R Markdown"

• I asked everyone to familiarize themselves with R Markdown.
• Success?

• Use the R Markdown cheat sheet for a nice overview on Markdown in RStudio.

• Try yourself:
• File -> New File -> R Markdown -> Document -> HTML
• Set output to different file formats (with the Knit button)

• Need to learn a bit of markdown syntax
• Take a look a the cheat sheet and/or reference guide

You can use Markdown to embed formatting instructions into your text. For example, you can make a word italicized by surrounding it in asterisks, bold by surrounding it in two asterisks, and monospaced (like code) by surrounding it in backticks:

*italics*, **bold**, `code`

You can turn a word into a link by surrounding it in hard brackets and then placing the link behind it in parentheses, like this:

[Columbia U](www.columbia.edu)

To create titles and headers, use leading hastags. The number of hashtags determines the header's level:

# First level header
## Second level header
### Third level header

To make a bulleted list in Markdown, place each item on a new line after an asterisk and a space, like this:

* item 1
* item 2
* item 3

You can make an ordered list by placing each item on a new line after a number followed by a period followed by a space.

1. item 1
2. item 2
3. item 3

You can also use the Markdown syntax to embed latex math equations into your reports. To embed an equation in its own centered equation block, surround the equation with two pairs of dollar signs like this,

$$1 + 1 = 2$$

To embed an equation inline, surround it with a single pair of dollar signs, like this: $1 + 1 = 2$

All standard Latex symbols work.

knitr is an engine for dynamic report generation with R and is used to convert (or "knit") R Markdown files into the desired output format.

• R code can be included as chunk with

  ```{r} ```

or inline with a single tickmark.

• R functions sometimes return messages, warnings, and even error messages. By default, R Markdown will include these messages in your report. You can use the message, warning and error options to prevent R Markdown from displaying these.

Three of the most popular chunk options are echo, eval and results.

• If echo = FALSE, R Markdown will not display the code in the final document (but it will still run the code and display its results unless told otherwise).

• If eval = FALSE, R Markdown will not run the code or include its results, (but it will still display the code unless told otherwise).

• If results = 'hide', R Markdown will not display the results of the code (but it will still run the code and display the code itself unless told otherwise).

• The Pandoc program (by John MacFarlane) renders R Markdown documents into the output we want.
• We can include specific options into the YAML header on top of our document to control this process.

Switch to the demo file Rmarkdown_demo.Rmd in the exercise folder for this week.

1. Interact with R in a single, seamless stream.
2. Iterate quickly on code and output; see code and output together.
3. Leave a clean, reproducible record of your analysis in a simple text file.
   
4. Document your analysis with rich, literate prose.
5. Share and publish easily.
6. One-click export to PDF, Word, etc.

Source: R Studio Webinar "Introducing Notebooks with R Markdown"

• html_document
• pdf_document
• word_document
• beamer_presentation / slidy_presentation / ioslides_presentation
• github_document

Note: see also description in exercise document.

• Confusing
• Prone to errors
• Collaboration
• Describe the changes
• Feature development

• Git
  • master-branch workflow
  • distributed (rather than centralized) version control
  • pull requests to manage/discuss updates
  • de facto standard on version control
• GitHub
  • Github is like facebook for programmers. Everyone’s on there.
  • open source
  • lowers the barriers to collaboration

Google Trends Comparison

• single largest host for Git repositories, and is the central point of collaboration for millions of developers and projects
• Free. Allows easy open source hosting. Private repositories available with your .edu email address.
• While Git is a command line tool, GitHub provides a web-based graphical interface.
• Provides access control and several collaboration features, such as a wikis and basic task management tools for every project.

• Use GitHub for your homework exercises
• Get the class material and resources on GitHub.
• Find useful repositories, packages, data, code, and tutorials: e.g. tidyverse, Hadley Wickham's "Advanced R" book etc.

• A clone is a copy of a repository that lives on your computer instead of on a website's server somewhere, or the act of making that copy

• A fork is a copy of another user's repository that you manage (and lives on your account).

• Forks let you make changes to a project without affecting the original repository.

• You can fetch updates from or submit changes to the original repository with pull requests.

• Go to: https://github.com/QMSS-G5072-2017/QMSS-G5072-Modern-Data-Structures
• Fork the course repository
• Fetch changes through Github Desktop.

• Pushing refers to sending your committed changes to a remote repository such as GitHub.com

• You can change files directly through the github.com website. Click the edit button, change, and the commit.

• Try out ideas for your project by creating a branch.
• Changes you make on a branch don't affect the master branch, so you're free to experiment and commit changes.

• Whenever you add, edit, or delete a file, you're making a commit, and adding them to your branch.
• Keeps track of your progress as you work on a branch.
• Transparent history of your work with associated commit message (i.e a description of your change).
• Allows you to roll back if things go awry.

• Pull Requests initiate discussion about your commits.
• Anyone can see exactly what changes would be merged if they accept your request.
• Using GitHub's @mention system in your Pull Request message to ask for feedback from your team.

• Discuss and review the changes.
• Continue to fix code and push up the change with new commits.
• GitHub will show your new commits and any additional feedback you may receive in the unified Pull Request view.

• Check your branch to verify it works.
• If your branch causes issues, you can roll it back by deploying the existing master again.

• Merge your code into the master branch.
• Pull Requests preserve a record of the historical changes to your code. Because they're searchable, they let anyone go back in time to understand why and how a decision was made.